How to reproduce:
1. Open the “PrefabVariantBug.zip“ project
2. Open the “SampleScene“
3. Select the “Reference” GameObject in the Hierarchy (observe the existing reference to “Prefab 3“ in the Script Component)
4. Double-click the “Prefab 3“ Prefab in the Project tab to enter the Prefab Edit Mode
5. Right-click the “Prefab 3” Prefab in the Hierarchy and select (Prefab > Unpack) once (for the base Prefab to become “Prefab 1”)
6. Save the changes and exit the Prefab Edit Mode
7. Select the “Reference“ GameObject in the Hierarchy
8. Observe the Inspector

Expected result: The “Prefab 3“ Prefab is still referenced in the Script Component
Actual result: “Missing (Game Object)“ is displayed in the Script Component

Reproducible in: 2021.3.42f1, 2022.3.41f1, 6000.0.14f1

Reproduced on: Windows 11 Pro (23H2)
Not reproduced on: No other environment tested

Note: If the variant is unpacked twice or completely the reference does not become missing